Showing papers by "Elizabeth A. Zimmer published in 1988"

Ribosomal Gene Structure, Variation and Inheritance in Maize and Its Ancestors

Abstract: We have examined the structure of nuclear genes coding for ribosomal RNAs in maize and its wild relatives, the teosintes and Tripsacum. Digestion of the rDNA (genes coding for 18S, 5.8S and 26S RNAs) with 15 restriction endonucleases (with six base pair recognition sites) yields essentially a single map for the approximately 10,000 repeat units within an individual plant or species. Both length and site variation were detected among species and were concentrated in the intergenic spacer region of the rDNA repeat unit. This result is in agreement with patterns of rDNA change observed among wheat and its relatives (Triticeae), and among vertebrate species. Digestion of these nuclear DNAs with BamHI and subsequent hybridization with a 5S RNA gene-specific probe allowed determination of the size of the 5S gene repeat unit in maize, teosintes, and Tripsacum. Groupings in the genus Zea were characterized by distinct repeat unit types five Tripsacum species examined shared a 260 base pair major repeat unit type. Additionally, several other restriction endonuclease cleavage patterns differentiated among the 5S DNAs within the genus Zea. The rDNA and 5S DNA restriction site variation among the species can be interpreted phylogenetically and agrees with biochemical, karyotypic, and morphological evidence that places maize closest to the Mexican teosintes. For both gene arrays, contributions from each parental genome can be detected by restriction enzyme analysis of progeny from crosses between maize and two distantly related teosintes, Zea luxurians or Zea diploperennis, but certain teosinte arrays were underrepresented in some of the hybrids.

Ribosomal RNA sequences for inferring phylogeny within the grass family (Poaceae)

Abstract: We have isolated RNA from nine different grass species and fromPsilotum, a modern representative of a primitive land plant lineage. By direct RNA sequencing with reverse transcriptase, we have determined the nucleotide sequence for five regions of the 18 S rRNA molecule and three regions of the 26 S rRNA molecule. Over 1 600 positions have been elucidated for each plant species. These sequences were aligned by computer and the variable positions were identified by inspection. The data from the variable positions were input into phylogenetic inference computer programs to generate an evolutionary relationship among the grass species. This evolutionary tree based on nucleotide sequence data was compared to a recent classification of thePoaceae based on morphological data.

Direct ribosomal RNA sequencing: Optimization of extraction and sequencing methods for work with higher plants

Abstract: R NA sequencing with reverse transcriptase, synthetic oligonucleotide primers and dideoxynucleotides is a particularly attractive choice for comparing ribosomal RNAs (rRNAs). The highly conserved nature of rRNAs allows identical oligonucleotide primers to be used successfully with templates from all lineages of eukaryotes (Zimmer and Sims, 1985; Jupe et al., 1988; Hamby and Zimmer, 1988). Similarly, \"universal\" primers can be synthesized for prokaryotic rRNAs (Lane et al., 1985, 1988). Direct sequencing methods for RNA offer the advantages of bypassing labor-intensive cloning steps and, in the case of multigene families, of providing sequence information on those genes which are actually transcribed. These methods are most applicable to systems in which a large percentage of the total RNA preparation is a specific, homogeneous product (e.g., ribosomal RNAs [Zimmer and Sims, 1985; Lane et al., 1985], abundant mRNAs [Martin et al., 1981; Tolan et al., 1984] and viral RNAs [Pace et al., 1986]). The application of rRNA sequencing to questions of evolutionary relationships is, therefore, an extremely active area of research. Ribosomal RNA sequences also offer some potential in diagnostics for species identification in cases of lineages

Nuclear ribosomal RNA genes and algal phylogeny--the Chlamydomonas example.

Abstract: The nuclear ribosomal RNA genes (rDNA) of Chlamydomonas reinhardtii, C. moewusii and C. eugametos were examined with restriction endonuclease fragment and direct rRNA sequencing analyses. These comparative molecular data confirm similarity between C. moewusii and C. eugametos , and dissimilarity between the strains and C. reinhardtii For C. moewusii and C. eugametos , the fragment analysis of digests with 16 (six base pair recognition site) restriction endonucleases revealed either no or minor differences. These minor differences appear to be confined to length and site variation in the rapidly evolving intergenic spacer region of the algal rDNA repeat unit. In contrast, patterns of digests for C. reinhardtii were completely different from those of C. moewusii and C. eugametos for all enzymes tested. Over two regions of the 18S ribosomal RNA (spanning approx. 300 bases) in C. moewusii and C. eugametos , we observed three possible base substitutions and no insertion/deletion events. The same comparison between C. reinhardtii and C. moewusii (or C. eugametos ) revealed 31 base substitutions and eight insertion/deletion events. Overall, the rDNA comparisons support the proposed conspecificity of C. moewusii and C. eugametos , as well as the hypothesis that intraspeciflc variation in the algal ribosomal RNA coding region is minimal and that comparisons of rDNA sequences at higher taxonomic levels can be useful indicators of algal phylogeny. The degree of difference in the sequences of the 188 coding region between C. reinhardtii and C. moeurusii or C. eugametos is comparable to that between an angiosperm and Equisetum and may reflect an ancient divergence between two species in one algal genus. This possibility then raises the fundamental question of “How should molecular evolutionary data be used in the review of traditional concepts of taxonomy?”